Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

G Albert Wu; Simon Prochnik; Jerry Jenkins; Jerome Salse; Uffe Hellsten; Florent Murat; Xavier Perrier; Manuel Ruiz; Simone Scalabrin; Javier Terol; Marco Aurélio Takita; Karine Labadie; Julie Poulain; Arnaud Couloux; Kamel Jabbari; Federica Cattonaro; Cristian Del Fabbro; Sara Pinosio; Andrea Zuccolo; Jarrod Chapman; Jane Grimwood; Francisco R Tadeo; Leandro H Estornell; Juan V Muñoz-Sanz; Victoria Ibanez; Amparo Herrero-Ortega; Pablo Aleza; Julián Pérez-Pérez; Daniel Ramón; Dominique Brunel; François Luro; Chunxian Chen; William G Farmerie; Brian Desany; Chinnappa Kodira; Mohammed Mohiuddin; Tim Harkins; Karin Fredrikson; Paul Burns; Alexandre Lomsadze; Mark Borodovsky; Giuseppe Reforgiato; Juliana Freitas-Astúa; Francis Quetier; Luis Navarro; Mikeal Roose; Patrick Wincker; Jeremy Schmutz; Michele Morgante; Marcos Antonio Machado; Manuel Talon; Olivier Jaillon; Patrick Ollitrault; Frederick Gmitter; Daniel Rokhsar

doi:10.1038/nbt.2906

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Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

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Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

G Albert Wu, Simon Prochnik, Jerry Jenkins, Jerome Salse, Uffe Hellsten, Florent Murat, Xavier Perrier, Manuel Ruiz, Simone Scalabrin, Javier Terol, …

Nature biotechnology, Vol.32(7), pp.656-662

01/07/2014

DOI: https://doi.org/10.1038/nbt.2906

PMID: 24908277

Résumé

Base Sequence

Breeding

Citrus - classification

Citrus - genetics

Conserved Sequence - genetics

Crops, Agricultural - genetics

Evolution, Molecular

Genetic Variation - genetics

Genome, Plant - genetics

Molecular Sequence Data

Sequence Analysis, DNA

Species Specificity

Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes--a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes--and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement.

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Détails

Titre: Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication
Créateurs - sans rôle: G Albert Wu - 1] US Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
Simon Prochnik - 1] US Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
Jerry Jenkins - HudsonAlpha Biotechnology Institute, Huntsville, Alabama, USA
Jerome Salse - Institut National de la Recherche Agronomique (INRA), Université Blaise Pascal (UBP) UMR 1095 Génétique, Diversité, Ecophysiologie des Céréales (GDEC), Clermont Ferrand, France
Uffe Hellsten - US Department of Energy Joint Genome Institute, Walnut Creek, California, USA
Florent Murat - Génétique, Diversité, Écophysiologie des Céréales
Xavier Perrier - Centre de Coopération Internationale en Recherche Agronomique pour le Développement
Manuel Ruiz - Centre de Coopération Internationale en Recherche Agronomique pour le Développement
Simone Scalabrin - Istituto di Genomica Applicata
Javier Terol - Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
Marco Aurélio Takita - Centro de Citricultura Sylvio Moreira, Instituto Agronômico (IAC), Cordeirópolis, Brazil
Karine Labadie - Genoscope
Julie Poulain - Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
Arnaud Couloux - Genoscope
Kamel Jabbari - Genoscope
Federica Cattonaro - Istituto di Genomica Applicata, Udine, Italy
Cristian Del Fabbro - Istituto di Genomica Applicata, Udine, Italy
Sara Pinosio - Istituto di Genomica Applicata
Andrea Zuccolo - 1] Istituto di Genomica Applicata, Udine, Italy. Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
Jarrod Chapman - US Department of Energy Joint Genome Institute, Walnut Creek, California, USA
Jane Grimwood - HudsonAlpha Biotechnology Institute, Huntsville, Alabama, USA
Francisco R Tadeo - Instituto Valenciano de Investigaciones Agrarias
Leandro H Estornell - Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
Juan V Muñoz-Sanz - Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
Victoria Ibanez - Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
Amparo Herrero-Ortega - Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
Pablo Aleza - Instituto Valenciano de Investigaciones Agrarias
Julián Pérez-Pérez - 1] Lifesequencing, Valencia, Spain. Secugen, Madrid, Spain
Daniel Ramón - Lifesequencing, Valencia, Spain
Dominique Brunel - 1] Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France. INRA, US 1279 Etude du Polymorphisme des Génomes Végétaux (EPGV), Evry, France
François Luro - INRA Génétique et Écophysiologie de la Qualité des Agrumes (GEQA), San Giuliano, France
Chunxian Chen - 1] Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, Florida, USA.
William G Farmerie - Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
Brian Desany - 454 Life Sciences, Roche, Branford, Connecticut, USA
Chinnappa Kodira - 454 Life Sciences, Roche, Branford, Connecticut, USA
Mohammed Mohiuddin - 454 Life Sciences, Roche, Branford, Connecticut, USA
Tim Harkins - 1] 454 Life Sciences, Roche, Branford, Connecticut, USA.
Karin Fredrikson - 454 Life Sciences, Roche, Branford, Connecticut, USA
Paul Burns - 1] Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA. School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
Alexandre Lomsadze - 1] Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA. School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
Mark Borodovsky - 1] Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA. School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA. Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
Giuseppe Reforgiato - Consiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA-ACM), Acireale, Italy
Juliana Freitas-Astúa - 1] Centro de Citricultura Sylvio Moreira, Instituto Agronômico (IAC), Cordeirópolis, Brazil. Embrapa Cassava and Fruits, Cruz das Almas, Brazil
Francis Quetier - 1] Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France. Département de Biologie, Université d'Evry, Evry, France
Luis Navarro - Instituto Valenciano de Investigaciones Agrarias
Mikeal Roose - Department of Botany and Plant Sciences, University of California, Riverside, Riverside, California, USA
Patrick Wincker - 1] Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France. Département de Biologie, Université d'Evry, Evry, France. Centre National de Recherche Scientifique (CNRS), Evry, France
Jeremy Schmutz - HudsonAlpha Biotechnology Institute, Huntsville, Alabama, USA
Michele Morgante - 1] Istituto di Genomica Applicata, Udine, Italy. Department of Agriculture and Environmental Sciences, University of Udine, Udine, Italy
Marcos Antonio Machado - Centro de Citricultura Sylvio Moreira, Instituto Agronômico (IAC), Cordeirópolis, Brazil
Manuel Talon - Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
Olivier Jaillon - Genoscope
Patrick Ollitrault - Centre de Coopération Internationale en Recherche Agronomique pour le Développement
Frederick Gmitter - Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, Florida, USA
Daniel Rokhsar - 1] US Department of Energy Joint Genome Institute, Walnut Creek, California, USA. Division of Genetics, Genomics and Development, University of California, Berkeley, Berkeley, California, USA
Détails de publication: Nature biotechnology, Vol.32(7), pp.656-662
Note de subvention: HG00783 / NHGRI NIH HHS R01 HG000783 / NHGRI NIH HHS
Identifiants: 99163589209311
Unité académique: Institut Amélioration Génétique & Adaptation des Plantes méditerranéennes & tropicales-AGAP
Langue: English
Type de ressource: Journal article